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Though nitrate enrichment in groundwater is a worldwide phenomenon and mainly related to human impact, processes leading to nitrate enrichment in scarcely inhabited semi-arid regions are not yet well understood. In those regions, elevated nitrate concentrations put additional pressure on the scarce water resources, as they pose a serious health risk. This study applies a multidisciplinary approach (hydrogeology, isotope hydrology, and geochemistry) to understand the origin and fate of nitrate in groundwater of the semi-arid Kalahari of Botswana. Our investigations suggest that nitrate in groundwater of the study area is of natural origin, leached from a pool in the unsaturated zone that was actively involved in the soil nitrogen cycle. The presence of active (minor) recharge was found, showing that nitrate may be transported into the groundwater under the present conditions. Yet, slow travel times of replenishing water and the low recharge amounts render the thick unsaturated zone into a long-term reservoir for nitrate. Being only little influenced by reactive processes, nitrate has a high persistency in the observed groundwater system. Concentration increases induced by the present land-Use do not yet appear to affect the groundwater quality but may within decades. (c) 2008 Elsevier Ltd. All rights reserved.